Dimensionality Reduction Plots

Cell-types

This two-dimensional embedding of cells should demonstrate spatial separation of major cell-types; if not, it may be useful to manually re-annotate cell-types with reference to cell-type associated marker genes, and/or revise dimensionality reduction and/or clustering parameters.

<b>Figure: UMAP_Liger plot of cell-types.</b> Each cell is coloured by annotated cell-type.

Figure: UMAP_Liger plot of cell-types. Each cell is coloured by annotated cell-type.

Top Cell-type Marker Genes Table

Top Cell-Type Marker Genes Plot

<b>Figure: Top marker genes for cells grouped by cell-type.</b> Point colour represents expression and size represents the fraction of cells within the group expressing the gene.

Figure: Top marker genes for cells grouped by cell-type. Point colour represents expression and size represents the fraction of cells within the group expressing the gene.

Clusters

Optimal clustering parameters should provide a level of granularity sufficient to identify minority cell-types as distinct numbered clusters. If any cluster encompasses an adjacent small, well-separated cluster, the clustering parameters should be revised to allow for the annotation of the potential minority cell-type.

<b>Figure: UMAP_Liger plot of clusters.</b> Each cell is coloured by annotated cluster.

Figure: UMAP_Liger plot of clusters. Each cell is coloured by annotated cluster.

Top Cluster Marker Genes Table

Top Cluster Marker Genes Plot

<b>Figure: Top marker genes for cells grouped by cluster.</b> Point colour represents expression and size represents the fraction of cells within the group expressing the gene.

Figure: Top marker genes for cells grouped by cluster. Point colour represents expression and size represents the fraction of cells within the group expressing the gene.

Manifest

<b>Figure: UMAP_Liger plot of cells by manifest.</b>

Figure: UMAP_Liger plot of cells by manifest.

Group

<b>Figure: UMAP_Liger plot of cells by group.</b>

Figure: UMAP_Liger plot of cells by group.

Sex

<b>Figure: UMAP_Liger plot of cells by sex.</b>

Figure: UMAP_Liger plot of cells by sex.

Cell-type Proportion Plots

These plots illustrate the absolute cell numbers and relative proportions of cell-types in the overall experiment (“all”), and within the groups: manifest, group, sex. To examine statistically significant differences in cell-type proportions, see the Dirichlet model results and report(s).

All

<b>Figure: Absolute cell-type numbers by all.</b>

Figure: Absolute cell-type numbers by all.

<b>Figure: Relative cell-type numbers by all.</b>

Figure: Relative cell-type numbers by all.

Manifest

<b>Figure: Absolute cell-type numbers by manifest.</b>

Figure: Absolute cell-type numbers by manifest.

<b>Figure: Relative cell-type numbers by manifest.</b>

Figure: Relative cell-type numbers by manifest.

Group

<b>Figure: Absolute cell-type numbers by group.</b>

Figure: Absolute cell-type numbers by group.

<b>Figure: Relative cell-type numbers by group.</b>

Figure: Relative cell-type numbers by group.

Sex

<b>Figure: Absolute cell-type numbers by sex.</b>

Figure: Absolute cell-type numbers by sex.

<b>Figure: Relative cell-type numbers by sex.</b>

Figure: Relative cell-type numbers by sex.

Cell-type Metric Plots

These plots summarize the distribution of various cell metrics (pc_mito, pc_ribo, total_counts, total_features_by_counts) for each cell-type.

pc_mito

<b>Figure: Average pc_mito by cell-type</b>.  Bars represent mean average +/- SEM.

Figure: Average pc_mito by cell-type. Bars represent mean average +/- SEM.

<b>Figure: Distributions of pc_mito by cell-type</b>.

Figure: Distributions of pc_mito by cell-type.

pc_ribo

<b>Figure: Average pc_ribo by cell-type</b>.  Bars represent mean average +/- SEM.

Figure: Average pc_ribo by cell-type. Bars represent mean average +/- SEM.

<b>Figure: Distributions of pc_ribo by cell-type</b>.

Figure: Distributions of pc_ribo by cell-type.

total_counts

<b>Figure: Average total_counts by cell-type</b>.  Bars represent mean average +/- SEM.

Figure: Average total_counts by cell-type. Bars represent mean average +/- SEM.

<b>Figure: Distributions of total_counts by cell-type</b>.

Figure: Distributions of total_counts by cell-type.

total_features_by_counts

<b>Figure: Average total_features_by_counts by cell-type</b>.  Bars represent mean average +/- SEM.

Figure: Average total_features_by_counts by cell-type. Bars represent mean average +/- SEM.

<b>Figure: Distributions of total_features_by_counts by cell-type</b>.

Figure: Distributions of total_features_by_counts by cell-type.


scFlow v0.5.1 – 2020-10-15 21:49:42

 

A report by scFlow